WASHINGTON — F.B.I. agents hunting for Pakistani spies in the United States last year began tracking Mohammed Tasleem, an attaché in the Pakistani Consulate in New York and a clandestine operative of Pakistan’s military spy agency, the Directorate for Inter-Services Intelligence.

Mr. Tasleem, they discovered, had been posing as an F.B.I. agent to extract information from Pakistanis living in the United States and was issuing threats to keep them from speaking openly about Pakistan’s government. His activities were part of what government officials in Washington, along with a range of Pakistani journalists and scholars, say is a systematic ISI campaign to keep tabs on the Pakistani diaspora inside the United States.

The F.B.I. brought Mr. Tasleem’s activities to Leon E. Panetta, then the director of the Central Intelligence Agency, and last April, Mr. Panetta had a tense conversation with Pakistan’s spymaster, Lt. Gen. Ahmed Shuja Pasha.

Within days, Mr. Tasleem was spirited out of the United States — a quiet resolution typical of the spy games among the world’s powers.

But some of the secrets of that hidden world became public last week when two Pakistani-Americans working for a charity that the F.B.I. believes is a front for Pakistan’s spy service were indicted. Only one was arrested; the other is still in Pakistan.

The investigation exposed one part of what American officials say is a broader campaign by the Pakistani spy agency, known as the ISI, to exert influence over lawmakers, stifle public dialogue critical of Pakistan’s military and blunt the influence of India, Pakistan’s longtime adversary.

American officials said that compared with countries like China and Russia — whose spies have long tried to steal American government and business secrets — the ISI’s operations here are less extensive and less sophisticated. And they are certainly far more limited than the C.I.A.’s activities inside Pakistan.

Even so, officials and scholars say the ISI campaign extends to issuing both tacit and overt threats against those who speak critically about the military.

The ISI is widely feared inside Pakistan because of these very tactics. For example, American intelligence officials believe that some ISI operatives ordered the recent killing of a Pakistani journalist, Saleem Shahzad.

At the same time, the Pakistani spy agency remains a close ally of the C.I.A. in the hunt for operatives with Al Qaeda. It is a relationship that often complicates the ability of the United States to put pressure on Pakistan to alter its tactics.

According to one American law enforcement official, the F.B.I. had originally hoped to arrest the two men working for the charity, the Kashmiri American Council, several times earlier this year but was told each time by the State Department or the C.I.A. that the arrests would only aggravate the frayed relations between the United States and Pakistan.

The indictments came as the C.I.A. was trying to negotiate the release of a Pakistani doctor who was jailed by the ISI on accusations that he had helped the Americans track down Osama bin Laden before his killing.

Washington has long been a venue for spy games between Pakistan and India as they have tried to win favor among lawmakers and White House officials. A senior official at Pakistan’s Embassy in Washington, speaking on the condition of anonymity, said it was customary for intelligence agencies to operate “outside the limelight,” adding that it was unfortunate that the ISI had become a subject of “demonization.”

“There is nothing that the ISI does in the United States that is not part of the normal function of intelligence agencies,” the embassy official said. “The ISI has never deliberately violated an understanding with the U.S. government or deliberately violated American law.”

Several Pakistani journalists and scholars in the United States interviewed over the past week said that they were approached regularly by Pakistani officials, some of whom openly identified themselves as ISI officials. The journalists and scholars said the officials caution them against speaking out on politically delicate subjects like the indigenous insurgency in Baluchistan or accusations of human rights abuses by Pakistani soldiers. The verbal pressure is often accompanied by veiled warnings about the welfare of family members in Pakistan, they said.

One Pakistani journalist, who like the others asked to be quoted anonymously because of concerns about his safety, recalled an episode in December 2006 in which a Pakistani man filmed a public discussion about Pakistan’s tribal areas at the Kennedy School of Government at Harvard. The event’s organizers later learned the man was from the ISI, the journalist said.

A second Pakistani author said that at several conferences and seminars in recent years, representatives from the spy agency made their presence known by asking threatening questions.

“The ISI guys will look into your eyes and will indirectly threaten you by introducing themselves,” the author said. “The ISI makes sure that they are present in every occasion relating to Pakistan, and in some cases they pay ordinary Pakistanis for attending events and pass them information.”

In a way, the activities of the ISI in the United States reflect the paranoia among officials in Islamabad that Pakistan’s influence in the United States has been eroding steadily because of a barrage of negative news accounts about Pakistan’s military and efforts by India to jockey for influence in Washington.

An American official who was briefed on the episode with Mr. Tasleem, the ISI operative, said that Mr. Tasleem collected information in a variety of ways, and that on at least one occasion he passed himself off as an F.B.I. agent to get information from one Pakistani living in the United States. An F.B.I. spokesman declined to comment.

The indictments last week were part of a broader F.B.I. investigation into how Pakistan’s government, including the ISI, has secretly funneled money into the United States to influence American policy about Kashmir, a region claimed both by India and Pakistan. The effort, American officials said, included lobbying and publicity activities by the Kashmiri American Council (also called the Kashmiri Center) and by donations to lawmakers.

Over the years, American investigators have uncovered numerous operatives spying for other countries — notably from China, Russia and Iraq. But before the Kasmiri American Council case, little had been said publicly about the ISI’s operations in the United States.

In recent years, the Justice Department has brought several cases against defendants charged with supporting terror groups that have historically had ties to the ISI, including Lashkar-e-Taiba, the militant group that carried out the 2008 attacks in Mumbai. But those cases, too, involved no allegations that the defendants were agents of the ISI.

Pir Zubair Shah contributed reporting from New York.

A version of this article appears in print on July 24, 2011, on page A1 of the New York edition with the headline: Pakistan Spies On Its Diaspora, Spreading Fear. Order Reprints|Today's Paper|Subscribe